diff --git a/scripts/align.py b/scripts/align.py
index 4620e62..902678a 100644
--- a/scripts/align.py
+++ b/scripts/align.py
@@ -11,28 +11,24 @@
 def main():
     parser = argparse.ArgumentParser(description="aligner")
 
-    parser.add_argument("-d", "--version-dir", required=True, help="Path to version dir")
-    parser.add_argument(
-        "-m", "--metadata_file", default=Constants.METADATA_XTAL_FILENAME.format(""), help="Metadata YAML file"
-    )
-    parser.add_argument("-a", "--assemblies", help="Assemblies YAML file")
+    parser.add_argument("-d", "--dir", help="Working directory")
 
-    parser.add_argument("-l", "--log-file", help="File to write logs to")
     parser.add_argument("--log-level", type=int, default=0, help="Logging level")
     parser.add_argument("--validate", action="store_true", help="Only perform validation")
 
     args = parser.parse_args()
 
-    if args.log_file:
-        log = args.log_file
+    if args.dir:
+        log = str(Path(args.dir) / 'aligner.log')
     else:
-        log = str(Path(args.version_dir).parent / 'aligner.log')
-        print("Using {} for log file".format(str(log)))
+        log = 'aligner.log'
 
     logger = utils.Logger(logfile=log, level=args.log_level)
     logger.info("aligner: ", args)
+    logger.info("Using {} for log file".format(str(log)))
+    utils.LOG = logger
 
-    a = Aligner(args.version_dir, args.metadata_file, args.assemblies, logger=logger)
+    a = Aligner(args.dir, logger=logger)
     num_errors, num_warnings = a.validate()
 
     if not args.validate:
diff --git a/scripts/collate.py b/scripts/collate.py
index c0d9abb..9b35588 100644
--- a/scripts/collate.py
+++ b/scripts/collate.py
@@ -1,23 +1,42 @@
 import argparse
 import shutil
+from pathlib import Path
 
 from xchemalign import utils
-from xchemalign.collator import Collator
+from xchemalign import setup
+from xchemalign.collator import Collator, _check_working_dir
 
 
 def main():
     parser = argparse.ArgumentParser(description="collator")
 
-    parser.add_argument("-c", "--config-file", default="config.yaml", help="Configuration file")
+    parser.add_argument("-d", "--dir", help="Working directory")
     parser.add_argument("-l", "--log-file", help="File to write logs to")
     parser.add_argument("--log-level", type=int, default=0, help="Logging level")
     parser.add_argument("-v", "--validate", action="store_true", help="Only perform validation")
+    parser.add_argument("--no-git-info", action="store_false", help="Don't add GIT info to metadata")
 
     args = parser.parse_args()
 
-    c = Collator(args.config_file, log_file=args.log_file, log_level=args.log_level)
+    if args.dir:
+        working_dir = Path(args.dir)
+    else:
+        working_dir = Path.cwd()
+
+    if _check_working_dir(working_dir):
+        print("Working dir does not seem to have been initialised - missing 'upload_current' symlink")
+        inp = input("Do you want the working dir to be initialised? (Y/N)")
+        if inp == "Y" or inp == "y":
+            print("Initialising working dir")
+            s = setup.Setup(args.dir)
+            s.run()
+        exit(1)
+
+    c = Collator(working_dir, log_file=args.log_file, log_level=args.log_level, include_git_info=args.no_git_info)
+
     logger = c.logger
     logger.info("collator: ", str(args))
+    utils.LOG = logger
 
     meta = c.validate()